************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 elnxx.phase.inp elnxx.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST elnxx.phase.out_freqs : haplotype frequency estimates elnxx.phase.out_pairs : most likely haplotype pairs for each individual elnxx.phase.out_recom : estimates of recombination parameters elnxx.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 40 Positions of loci: 135 171 400 461 944 1015 2491 2608 2721 2766 4152 4788 5266 8471 11617 11740 13676 13951 14106 14268 14753 14861 16327 28646 30191 30259 31527 31683 32971 34302 35252 35713 35726 40282 40505 41999 42178 43009 43167 43702 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file elnxx.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ACITCGGGGCCDATGGGCGGTGGCGTTATGGTCGCAADGA 22.000000 2 ACITCGGGGCCDATGGGCGGTGGCGTTATGGTCGTAGDCA 1.000000 3 ACITCGGGGCCDATGGGCGGTGGCGTTATGGCTGCAADGA 1.000000 4 ACITCGGGGCCDATGGGCGGTGGCGTTACGGTCGCAAICA 1.000000 5 ACITCGGGGCCDATGGGCGGTGGCGTTACGATCGCAADGA 2.000000 6 ACITCGGGGCCDATGGGCGGTGGCGTTACGATCGCGAICG 3.000000 7 ACITCGGGGCCDATGGGCGGTGGCGTTACGATCACAAIGA 1.000000 8 ACITCGGGGCCDATGGGCGGTGGCGTTGTGGTCGCAADGA 1.000000 9 ACITCGGGGCCDATGGGCGGTGGCGTTGTGGTCGTAGICA 2.000000 10 ACITCGGGGCCDATGGGCGGTGGCGTCATGGTCGCAADGA 4.000000 11 ACITCGGGGCCDATGGGCGGTGGCGTCACGATCGCGAICG 4.000000 12 ACITCGGGGCCDATGGACGGTGGCGTTATGGTCGCAADGA 1.000000 13 ACITCGGGGCCDATGGACGGTGACGTTATGGTCGCAADGA 1.000000 14 ACITCGGGGCCDATGGACGGTGACGTCATGGTCGTAGICA 3.000000 15 ACITCGGGGCCDATGGACGGTGACGTCACCATCACAAIGA 1.000000 16 ACITCGGGGTCDATGGGCGGTGGCGTTATGGTCGCAADGA 2.000000 17 ACITCGGGGTCDATGGGCGGTGGCGTTGTGGTCGCAADGA 4.000000 18 ACITCGGGGTCDATGGGCGGTGGCGTTGCGGTCGCAADGA 1.000000 19 ACITCGAGGCCDGTGGGCGGTGGTATCATGGTCGTAGICA 1.000000 20 ACITCAGTACCIGCAAGTGACAGCGCTACGGTCGCGAICG 1.000000 21 ACITTGGGGCCDATGGACGGTGACGTCATGGTCGCAADGA 1.000000 22 ACITTGAGGCCDGTGGGCGGTGGTATCATGGTCGCAADGA 6.000000 23 ACITTGAGGCCDGTGGGCGGTGGTATCATGGTCGCGAICG 1.000000 24 ACITTGAGGCCDGTGGGCGGTGGTATCATGGTTGCAADGA 1.000000 25 ACITTGAGGCCDGTGGGCGGTGGTATCATGGCTGCAADGA 6.000000 26 ACITTGAGGCTDGTGGGCGGTGGTATCATGGCTGCAADGA 1.000000 27 GCITCGGGGCCDATGGGCTGTGGCGCTACGATCGCGAICG 1.000000 28 GCITCGGGGCCDATGGGCTGTGGCGCTACCATCACAAIGA 3.000000 29 GCITCGGGGCCDATGGGCTGTGGCGCCATGGTCGCAADGA 2.000000 30 GCITCGGGGCCDATGGGCTGTGGCGCCACGATCGCAAIGA 1.000000 31 GCITCGGGGCCDATGGGCTGTGGCGCCACGATCACAAIGA 1.000000 32 GCITCGGGGCCDATGGGCTGTGGCGTTGTCGTCGCAADGA 1.000000 33 GCICCGGGGCCDATGGGCGGTGGCGTTACGATCGCGADCG 1.000000 34 GADCCGGTACTDATGGGCGGTGGCGTTGTGGTCGCAADGA 1.000000 35 GADCCAGTGCTDATGGGCGGTGGCGTCATGGTCGTAGICA 1.000000 36 GADCCAGTACCIGCAAGTGACAGCGCTACGGTCGCGAICG 1.000000 37 GADCCAGTACCIGCAAGTGACAGCGCCATGGTCGTAGICA 3.000000 38 GADCCAGTACTDATGGGCGGTGGCGTTGTGGTCGCAADGA 5.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,17) DY02: (6,27) DY03: (9,18) DY04: (25,32) DY05: (1,37) DY06: (5,37) DY07: (2,33) DY08: (1,20) DY09: (34,38) DY10: (5,38) DY11: (11,37) DY12: (16,17) DY13: (26,38) DY14: (8,10) DY15: (9,38) DY16: (6,22) DY17: (10,23) DY18: (6,16) DY19: (1,11) DY20: (1,17) DY21: (11,36) DY22: (11,35) DY23: (17,38) DY24: (4,25) E101: (1,1) E102: (1,25) E103: (1,29) E104: (7,22) E105: (1,1) E106: (1,25) E107: (1,22) E108: (1,1) E109: (1,14) E110: (12,15) E111: (19,22) E112: (10,28) E113: (22,22) E114: (1,28) E115: (1,10) E116: (14,21) E117: (24,28) E118: (1,31) E119: (13,25) E120: (29,30) E121: (1,25) E122: (1,14) E123: (1,3) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 A C I T C G G G G C C D A T G G G C G G T G G C G T T A T G G T C G C A A D G A A C I T C G G G G T C D A T G G G C G G T G G C G T T G T G G T C G C A A D G A 0 DY02 A C I T C G G G G C C D A T G G G C G G T G G C G T T A C G A T C G C G A I C G G C I T C G G G G C C D A T G G G C T G T G G C G C T A C G [A] T C G C G A I C G 0 DY03 A C I T C G G G G (C) C D A T G G G C G G T G G C G T T G (T) G G T C G T A G I C A A C I T C G G G G (T) C D A T G G G C G G T G G C G T T G (C) G [G] T C G C A A D G A 0 DY04 A C I T T G A G G C C D G T G G G C G G T G G T A T C A T (G) G C T G C A A D G A G C I T C G G G G C C D A T G G G C T G T G G C G T T G T (C) G T C G C A A D G A 0 DY05 A C I T C G G G G C C D A T G G G C G G T G G C G T T A T G G T C G C A A D G A G A D C C A G T A C C I G C A A G T G A C A G C G C C A T G G T C G T A G I C A 0 DY06 A C I T C G G G G C C D A T G G G C G G T G G C G T T A C G [A] T C G C A A D G A G A D C C A G T A C C I G C A A G T G A C A G C G C C A T G G T C G T A G I C A 0 DY07 (A) C I (T) C G G G G C C D A T G G G C G G T G G C G T T A T G G T C G T A G D C A (G) C I (C) C G G G G C C D A T G G G C G G T G G C G T T A C G [A] T C G C G A D C G 0 DY08 A C I T C G G G G C C D A T G G G C G G T G G C G T T A T G G T C G C A A D G A A C I T C A G T A C C I G C A A G T G A C A G C G C T A C G G T C G C G A I C [G] 0 DY09 G A D C C G G T A C T D A T G G G C G G T G G C G T T G T G G T C G C A A D G A G A D C C A G T A C T D A T G G G C G G T G G C G T T G T G G T C G C A A D G A 0 DY10 A C I T C G G G G C C D A T G G G C G G T G G C G T T A (C) G (A) T C G C A A D G A G A D C C A G T A C T D A T G G G C G G T G G C G T T G (T) G (G) T C G C A A D G A 0 DY11 A C I T C G G G G C C D A T G G G C G G T G G C G T C A C G A T C G C G A I C G G A D C C A G T A C C I G C A A G T G A C A G C G C C A T G G T C G T A G I C A 0 DY12 A C I T C G G G G T C D A T G G G C G G T G G C G T T A T G G T C G C A A D G A A C I T C G G G G T C D A T G G G C G G T G G C G T T G T G G T C G C A A D G A 0 DY13 A C I T T G A G G C T D G T G G G C G G T G G T A T C A T G G C T G C A A D G A G A D C C A G T A C T D A T G G G C G G T G G C G T T G T G G T C G C A A D G A 0 DY14 A C I T C G G G G C C D A T G G G C G G T G G C G T T G T G G T C G C A A D G A A C I T C G G G G C C D A T G G G C G G T G G C G T C A T G G T C G C A A D G A 0 DY15 A C I T C G G G G C C D A T G G G C G G T G G C G T T G T G G T C G (T) A (G) (I) (C) A G A D C C A G T A C T D A T G G G C G G T G G C G T T G T G G T C G (C) A (A) (D) (G) A 0 DY16 A C I T (C) G (G) G G C C D (A) T G G G C G G T G G (C) (G) T (T) A C G A T C G C G A I C G A C I T (T) G (A) G G C C D (G) T G G G C G G T G G (T) (A) T (C) A T G G T C G C A A D G A 0 DY17 A C I T (C) G (G) G G C C D (A) T G G G C G G T G G (C) (G) T C A T G G T C G C A A D G A A C I T (T) G (A) G G C C D (G) T G G G C G G T G G (T) (A) T C A T G G T C G C G A I C G 0 DY18 A C I T C G G G G (C) C D A T G G G C G G T G G C G T T A C G A T C G C G A I C G A C I T C G G G G (T) C D A T G G G C G G T G G C G T T A T G G T C G C A A D G A 0 DY19 A C I T C G G G G C C D A T G G G C G G T G G C G T (T) A T G G T C G C A A D G A A C I T C G G G G C C D A T G G G C G G T G G C G T (C) A C G A T C G C G A I C G 0 DY20 A C I T C G G G G C C D A T G G G C G G T G G C G T T A T G G T C G C A A D G A A C I T C G G G G T C D A T G G G C G G T G G C G T T G T G G T C G C A A D G A 0 DY21 (A) (C) (I) (T) C G G G G C C D A T G G G C G G T G G C G T C A C G A T C G C G A I C G (G) (A) (D) (C) C A G T A C C I G C A A G T G A C A G C G C T A C G G T C G C G A I C [G] 0 DY22 (A) (C) (I) (T) C (G) G (G) G C (C) D A T G G G C G G T G G C G T C A C G A T C G C G A I C G (G) (A) (D) (C) C (A) G (T) G C (T) D A T G G G C G G T G G C G T C A T G G T C G T A G I C A 0 DY23 A C I T C G G G G T C D A T G G G C G G T G G C G T T G T G G T C G C A A D G A G A D C C A G T A C T D A T G G G C G G T G G C G T T G T G G T C G C A A D G A 0 DY24 A C I T C G G G G C C D A T G G G C G G T G G C G T T A (C) G G T C G C A A (I) (C) A A C I T T G A G G C C D G T G G G C G G T G G T A T C A (T) G G C T G C A A (D) (G) A 0 E101 A C I T C G G G G C C D A T G G G C G G T G G C G T T A T G G T C G C A A D G A A C I T C G G G G C C D A T G G G C G G T G G C G T T A T G G T C G C A A D G A 0 E102 A C I T C G G G G C C D A T G G G C G G T G G C G T T A T G G (T) (C) G C A A D G A A C I T T G A G G C C D G T G G G C G G T G G T A T C A T G G (C) (T) G C A A D G A 0 E103 A C I T C G G G G C C D A T G G G C G G T G G C G T T A T G G T C G C A A D G A G C I T C G G G G C C D A T G G G C T G T G G C G C C A T G G T C G C A A D G A 0 E104 A C I T C G G G G C C D A T G G G C G G T G G C G T T A (C) G (A) T C (A) C A A (I) G A A C I T T G A G G C C D G T G G G C G G T G G T A T C A (T) G (G) T C (G) C A A (D) G A 0 E105 A C I T C G G G G C C D A T G G G C G G T G G C G T T A T G G T C G C A A D G A A C I T C G G G G C C D A T G G G C G G T G G C G T T A T G G T C G C A A D G A 0 E106 A C I T C G G G G C C D A T G G G C G G T G G C G T T A T G G (T) (C) G C A A D G A A C I T T G A G G C C D G T G G G C G G T G G T A T C A T G G (C) (T) G C A A D G A 0 E107 A C I T C G G G G C C D A T G G G C G G T G G C G T T A T G G T C G C A A D G A A C I T T G A G G C C D G T G G G C G G T G G T A T C A T G G T C G C A A D G A 0 E108 A C I T C G G G G C C D A T G G G C G G T G G C G T T A T G G T C G C A A D G A A C I T C G G G G C C D A T G G G C G G T G G C G T T A T G G T C G C A A D G A 0 E109 A C I T C G G G G C C D A T G G G C G G T G G C G T T A T G G T C G C A A D G A A C I T C G G G G C C D A T G G A C G G T G A C G T C A T G G T C G T A G I C A 0 E110 A C I T C G G G G C C D A T G G A C G G T G (G) C G T (T) A T G G T C G C A A D G A A C I T C G G G G C C D A T G G A C G G T G (A) C G T (C) A C C A T C A C A A I G A 0 E111 A C I T (C) G A G G C C D G T G G G C G G T G G T A T C A T G G T C G T A G I C A A C I T (T) G A G G C C D G T G G G C G G T G G T A T C A T G G T C G C A A D G A 0 E112 A C I T C G G G G C C D A T G G G C G G T G G C G T C A T G G T C G C A A D G A G C I T C G G G G C C D A T G G G C T G T G G C G C T A C C A T C A C A A I G A 0 E113 A C I T T G A G G C C D G T G G G C G G T G G T A T C A T G G T C G C A A D G A A C I T T G A G G C C D G T G G G C G G T G G T A T C A T G G T C G C A A D G A 0 E114 A C I T C G G G G C C D A T G G G C G G T G G C G T T A T G G T C G C A A D G A G C I T C G G G G C C D A T G G G C T G T G G C G C T A C C A T C A C A A I G A 0 E115 A C I T C G G G G C C D A T G G G C G G T G G C G T T A T G G T C G C A A D G A A C I T C G G G G C C D A T G G G C G G T G G C G T C A T G G T C G C A A D G A 0 E116 A C I T (C) G G G G C C D A T G G A C G G T G A C G T C A T G G T C G T A G I C A A C I T (T) G G G G C C D A T G G A C G G T G A C G T C A T G G T C G C A A D G A 0 E117 A C I T T G A G G C C D G T G G G C G G T G G T A T C A T G G T (T) G C A A D G A G C I T C G G G G C C D A T G G G C T G T G G C G C T A C C A T (C) A C A A I G A 0 E118 (A) C I T C G G G G C C D A T G G G C (G) G T G G C G (T) (T) A T G G T C G C A A D G A (G) C I T C G G G G C C D A T G G G C (T) G T G G C G (C) (C) A C G A T C [A] C A A I G A 0 E119 A C I T C G G G G C C D A T G G A C G G T G A C G T (T) A T G G (T) (C) G C A A D G A A C I T T G A G G C C D G T G G G C G G T G G T A T (C) A T G G (C) (T) G C A A D G A 0 E120 G C I T C G G G G C C D A T G G G C T G T G G C G C C A T G G T C G C A A D G A G C I T C G G G G C C D A T G G G C T G T G G C G C C A C G [A] T C [G] C A A [I] G A 0 E121 A C I T C G G G G C C D A T G G G C G G T G G C G T T A T G G (T) (C) G C A A D G A A C I T T G A G G C C D G T G G G C G G T G G T A T C A T G G (C) (T) G C A A D G A 0 E122 A C I T C G G G G C C D A T G G G C G G T G G C G T T A T G G T C G C A A D G A A C I T C G G G G C C D A T G G A C G G T G A C G T C A T G G T C G T A G I C A 0 E123 A C I T C G G G G C C D A T G G G C G G T G G C G T T A T G G T C G C A A D G A A C I T C G G G G C C D A T G G G C G G T G G C G T T A T G G C T G C A A D G A END BESTPAIRS1 Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in [] with phase known positions indicated by = BEGIN BESTPAIRS2 0 DY01 = = = = = = = = = C = = ? = = = = = = = = ? = = = ? = A = = ? = = = = = = = = ? = = = = = = = = = T = = ? = = = = = = = = ? = = = ? = G = = ? = = = = = = = = ? 0 DY02 A = = = = = = ? ? ? ? = ? = = = = = G = = = = = = T = = = = ? = = = = = = = = ? G = = = = = = ? ? ? ? = ? = = = = = T = = = = = = C = = = = ? = = = = = = = = ? 0 DY03 = = = = = = = = = (C) = = ? = = = ? = = = = = = = ? = = = (T) = ? = = = T = G I C ? = = = = = = = = = (T) = = ? = = = ? = = = = = = = ? = = = (C) = ? = = = C = A D G ? 0 DY04 A = = = T = A = = = = = G = = = ? = G = = = = T A = C A = (G) ? C T = = = = = = ? G = = = C = G = = = = = A = = = ? = T = = = = C G = T G = (C) ? T C = = = = = = ? 0 DY05 A C I T = G = G G = = D ? T G G ? C = G T G = = = T T = = = ? = = = ? = A D ? ? G A D C = A = T A = = I ? C A A ? T = A C A = = = C C = = = ? = = = ? = G I ? ? 0 DY06 A C I T = G = G G = = D A T G G = C = G T G = = = T T = C = ? = = = C = A D ? ? G A D C = A = T A = = I G C A A = T = A C A = = = C C = T = ? = = = T = G I ? ? 0 DY07 (A) = = (T) = = = ? = = = = ? ? = ? = = = = = = = = ? ? = = T = ? = = = T A G = = ? (G) = = (C) = = = ? = = = = ? ? = ? = = = = = = = = ? ? = = C = ? = = = C G A = = ? 0 DY08 = = = = = G = G G ? = D A T G G = C = G T G ? = = T = = T = ? = = = = A = D G ? = = = = = A = T A ? = I G C A A = T = A C A ? = = C = = C = ? = = = = G = I C ? 0 DY09 = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? 0 DY10 A C I T = G = G G = C = = = = = = = = = = = = = = ? ? ? (C) = (A) ? ? = = = = = = = G A D C = A = T A = T = = = = = = = = = = = = = = ? ? ? (T) = (G) ? ? = = = = = = = 0 DY11 A C I T = G = G G = = D A T G G = C = G T G = = = T = = C = A = = = C G A = = G G A D C = A = T A = = I G C A A = T = A C A = = = C = = T = G = = = T A G = = A 0 DY12 = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = 0 DY13 A C I T T G A G G = = = G = = = = = = = = = = T A = C A = = = C T = = = = = = ? G A D C C A G T A = = = A = = = = = = = = = = C G = T G = = = T C = = = = = = ? 0 DY14 = = = = = = = = = = = = = = = = = = = = = = = = = = T G = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = C A = = = = = = = = = = = ? 0 DY15 A C I T = G = G G = C = = = = = = = = = = = = = = = = = = = = = = = (T) = (G) (I) (C) ? G A D C = A = T A = T = = = = = = = = = = = = = = = = = = = = = = = (C) = (A) (D) (G) ? 0 DY16 = = = = (C) = (G) = = = = = (A) = = = ? = = = = = ? (C) (G) = (T) = C = A = = = = G = I C ? = = = = (T) = (A) = = = = = (G) = = = ? = = = = = ? (T) (A) = (C) = T = G = = = = A = D G ? 0 DY17 = = = = (C) = (G) = = = = = (A) = = = = = = = = = = (C) (G) = = = = = = = = = = A = D G ? = = = = (T) = (A) = = = = = (G) = = = = = = = = = = (T) (A) = = = = = = = = = = G = I C ? 0 DY18 = = = = = = = = = (C) = = = = = = = = = = = = = = = = = = C = A = = = = G = I C G = = = = = = = = = (T) = = = = = = = = = = = = = = = = = = T = G = = = = A = D G A 0 DY19 = = = = = = = = = = = = = = = = = = = = = = = = = = (T) = T = G = = = = A = D G ? = = = = = = = = = = = = = = = = = = = = = = = = = = (C) = C = A = = = = G = I C ? 0 DY20 = = = = = = = = = C = = = = = = = = = = = = = = = = = A = = = = = = = = = = = ? = = = = = = = = = T = = = = = = = = = = = = = = = = = G = = = = = = = = = = = ? 0 DY21 (A) (C) (I) (T) ? ? = G G = = D A T G G = C = G T G = = = T C = = = A = = = = = = = = ? (G) (A) (D) (C) ? ? = T A = = I G C A A = T = A C A = = = C T = = = G = = = = = = = = ? 0 DY22 (A) (C) (I) (T) = (G) = (G) = = (C) = = = = = = = = = = = = = = = = = C = ? = = = C G A = = ? (G) (A) (D) (C) = (A) = (T) = = (T) = = = = = = = = = = = = = = = = = T = ? = = = T A G = = ? 0 DY23 A C I T = G = G G T C = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? G A D C = A = T A C T = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? 0 DY24 = = = = C = G = = = = = A = = = = = = = = = = C G = ? ? (C) = = T C = = = = (I) (C) = = = = = T = A = = = = = G = = = = = = = = = = T A = ? ? (T) = = C T = = = = (D) (G) = 0 E101 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E102 = = = = C = G = = = = = A = = = = = = = = = = C G = T = = = = (T) (C) = = = = = = = = = = = T = A = = = = = G = = = = = = = = = = T A = C = = = = (C) (T) = = = = = = = 0 E103 A = = = = = = = = = = = = = = = = = G = = = = = = T T = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = T = = = = = = C C = = = = = = = = = = = = = 0 E104 = = = = C = G = = = = = A = = = = = = = = = = C G = T = (C) = (A) = = (A) = = = (I) = = = = = = T = A = = = = = G = = = = = = = = = = T A = C = (T) = (G) = = (G) = = = (D) = = 0 E105 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? 0 E106 = = = = C = G = = = = = A = = = = = = = = = = C G = T = = = = (T) (C) = = = = = = = = = = = T = A = = = = = G = = = = = = = = = = T A = C = = = = (C) (T) = = = = = = = 0 E107 = = = = C = G = = = = = A = = = = = = = = = = C G = T = = = = = = = = = = = = = = = = = T = A = = = = = G = = = = = = = = = = T A = C = = = = = = = = = = = = = 0 E108 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E109 = = = = = = = = = = = = = = = = G = = = = = G = = = T = = = = = = = C = A D G ? = = = = = = = = = = = = = = = = A = = = = = A = = = C = = = = = = = T = G I C ? 0 E110 = = = = = = = = = = = = = = = = = = = = = = (G) = = = (T) = T G G = = G = = = D = ? = = = = = = = = = = = = = = = = = = = = = = (A) = = = (C) = C C A = = A = = = I = ? 0 E111 = = = = (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = G I C = = = = = (T) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = A D G = 0 E112 A = = = = = = = = = = = = = = = = = G = = = = = = T C = T G G = = G = = = D = ? G = = = = = = = = = = = = = = = = = T = = = = = = C T = C C A = = A = = = I = ? 0 E113 = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = ? = = = = = ? = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = ? = = = = = ? 0 E114 A = = = = = = = = = = = = = = = = = G = = = = = = T = = T G G = = G = = = D = ? G = = = = = = = = = = = = = = = = = T = = = = = = C = = C C A = = A = = = I = ? 0 E115 = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = ? 0 E116 ? ? ? ? (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = G I C = ? ? ? ? (T) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = A D G = 0 E117 A = = = T = A = = = = = G = = = = = G = = = = T A T C = T G G = (T) G = = = D = = G = = = C = G = = = = = A = = = = = T = = = = C G C T = C C A = (C) A = = = I = = 0 E118 (A) = = = = = = = = = = = = = = = = = (G) = = = = = = (T) (T) = T = ? = = ? = = = D = ? (G) = = = = = = = = = = = = = = = = = (T) = = = = = = (C) (C) = C = ? = = ? = = = I = ? 0 E119 = = = = C = G = = = = = A = = = A = = = = = A C G = (T) = = = = (T) (C) = = = = = = ? = = = = T = A = = = = = G = = = G = = = = = G T A = (C) = = = = (C) (T) = = = = = = ? 0 E120 = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = ? = = ? = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = ? = = ? = = = ? ? = 0 E121 = = = = C = ? = = = = = A = = = = = = = = = = C G = T = = = = (T) (C) = = = = ? = ? = = = = T = ? = = = = = G = = = = = = = = = = T A = C = = = = (C) (T) = = = = ? = ? 0 E122 = = = = = = = = = = = = = = = = G = = = = = G = = = T = = = = = = = C = A D G ? = = = = = = = = = = = = = = = = A = = = = = A = = = C = = = = = = = T = G I C ? 0 E123 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T C = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C T = = = = = = ? END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = = = = = = = = 0.95 = = ? = = = = = = = = ? = = = ? = 1.00 = = ? = = = = = = = = ? 1.00 = = = = = = ? ? ? ? = ? = = = = = 1.00 = = = = = = 1.00 = = = = ? = = = = = = = = ? = = = = = = = = = 0.87 = = ? = = = ? = = = = = = = ? = = = 0.66 = ? = = = 1.00 = 1.00 1.00 1.00 ? 1.00 = = = 1.00 = 1.00 = = = = = 1.00 = = = ? = 1.00 = = = = 1.00 1.00 = 1.00 1.00 = 0.54 ? 0.94 0.94 = = = = = = ? 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = 1.00 ? 1.00 1.00 1.00 ? 1.00 = 1.00 1.00 1.00 = = = 1.00 1.00 = = = ? = = = ? = 1.00 1.00 ? ? 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = = = 1.00 1.00 = 1.00 = ? = = = 1.00 = 1.00 1.00 ? ? 0.56 = = 0.61 = = = ? = = = = ? ? = ? = = = = = = = = ? ? = = 1.00 = ? = = = 1.00 1.00 1.00 = = ? = = = = = 1.00 = 1.00 1.00 ? = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 ? = = 1.00 = = 0.99 = ? = = = = 0.99 = 0.99 0.99 ? = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = ? ? ? 0.88 = 0.88 ? ? = = = = = = = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = = = 1.00 = = 1.00 = 1.00 = = = 1.00 1.00 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = = = = = = = = = = 1.00 1.00 = 1.00 1.00 = = = 0.94 0.94 = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = 0.92 1.00 = = = = = = = = = = = ? 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = 0.83 = 0.83 0.83 0.83 ? = = = = 0.78 = 0.78 = = = = = 0.78 = = = ? = = = = = ? 0.78 0.78 = 0.72 = 1.00 = 1.00 = = = = 0.95 = 0.95 0.95 ? = = = = 0.57 = 0.57 = = = = = 0.57 = = = = = = = = = = 0.57 0.57 = = = = = = = = = = 0.97 = 0.97 0.97 ? = = = = = = = = = 0.69 = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = = = 1.00 = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = 0.86 = 0.99 = 0.99 = = = = 1.00 = 1.00 1.00 ? = = = = = = = = = 0.95 = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = ? 0.88 0.88 0.88 0.88 ? ? = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = = = 1.00 1.00 = = = 0.96 = = = = = = = = ? 0.90 0.90 0.90 0.90 = 0.90 = 0.90 = = 0.90 = = = = = = = = = = = = = = = = = 1.00 = ? = = = 1.00 1.00 1.00 = = ? 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = 0.99 = 0.99 = = = = = 0.99 = = = = = = = = = = 0.99 0.99 = ? ? 0.82 = = 0.93 0.93 = = = = 0.57 0.57 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = = = = 1.00 = = = = = = = = = = 1.00 1.00 = 0.98 = = = = 0.83 0.83 = = = = = = = 1.00 = = = = = = = = = = = = = = = = = 1.00 = = = = = = 1.00 0.94 = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = = = = 1.00 = = = = = = = = = = 1.00 1.00 = 1.00 = 0.60 = 0.60 = = 0.50 = = = 0.50 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = 1.00 = 1.00 = = = = = 1.00 = = = = = = = = = = 1.00 1.00 = 0.98 = = = = 0.83 0.83 = = = = = = = = = = = 1.00 = 1.00 = = = = = 1.00 = = = = = = = = = = 1.00 1.00 = 0.99 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.92 = = = = = 0.92 = = = 0.95 = = = = = = = 1.00 = 1.00 1.00 1.00 ? = = = = = = = = = = = = = = = = = = = = = = 0.57 = = = 0.56 = 1.00 1.00 1.00 = = 1.00 = = = 1.00 = ? = = = = 0.50 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 = 0.94 = = = = = = = = = = = = = = = = = 0.94 = = = = = = 0.94 0.91 = 1.00 0.99 1.00 = = 1.00 = = = 1.00 = ? = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = ? = = = = = ? 0.99 = = = = = = = = = = = = = = = = = 0.99 = = = = = = 0.99 = = 1.00 1.00 1.00 = = 1.00 = = = 1.00 = ? = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = ? ? ? ? ? 0.50 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 = 1.00 = = = 1.00 = 1.00 = = = = = 1.00 = = = = = 1.00 = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = 0.63 1.00 = = = 1.00 = = 0.85 = = = = = = = = = = = = = = = = = 0.85 = = = = = = 0.85 0.84 = 1.00 = ? = = ? = = = 1.00 = ? = = = = 0.99 = 1.00 = = = = = 1.00 = = = 1.00 = = = = = 1.00 1.00 1.00 = 0.90 = = = = 0.86 0.86 = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = ? = = ? = = = ? ? = = = = = 1.00 = ? = = = = = 1.00 = = = = = = = = = = 1.00 1.00 = 0.98 = = = = 0.84 0.84 = = = = ? = ? = = = = = = = = = = = = = = = = 0.93 = = = = = 0.93 = = = 0.95 = = = = = = = 1.00 = 1.00 1.00 1.00 ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = = = = ? END PHASEPROBS